You got that backwards buddy. They had no idea who the guy with the virus was until the man that released the virus in the hotel, now in CTU custody and being interrogated by Michelle, IDs his photo. Jack's only role was in helping CTU refine the search parameters and then IDing the guy's name based on the photo. Jack then calls MI6 who in turn gives him info about the madame's relationship to their ex-agent, when Jack decides to pick her up and bring her in to MI6 for questioning.
Michelle demanded from Tony suicide pills used by field agents should they be captured and subject to torture to ease the suffering of the infected hotel guests. Tony was caught by Chappelle fetching the pills but was given the go-ahead despite the fact it's against "every regulation in the book".
The ordering of Chappelle's death was incidental - they found out that Chappelle's following the money trail of their operation and must be stopped.